Synthetic spike-in standards for RNA-seq experiments

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Items 101–200 of 659

1. Single Cell RNA Sequencing of Rare Immune Cell Populations
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2. Analysis and correction of compositional bias in sparse sequencing count data
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3. Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing
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4. Plant Systems Biology at the Single-Cell Level
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5. Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease
   Thomas A. Ray, Kelly Cochran, Christopher Kozlowski, Jingjing Wang, Graham C Alexander, Martha A. Cady, William J. Spencer, Philip A. Ruzycki, Brian S. Clark, Annelies Laeremans et al. · 2020 · Nature Communications
6. Portraying breast cancers with long noncoding RNAs
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7. Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression
   Bjoern Gaertner, Jeffrey J. Johnston, Kai Chen, Nina Wallaschek, Ariel Paulson, Alexander S. Garruss, Karin Gaudenz, Bony De Kumar, Robb K. Krumlauf, Julia Zeitlinger · 2012 · Cell Reports
8. Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition
   Yun Huang, Jong Kyoung Kim, Dang Vinh Do, Caroline Guat Lay Lee, Christopher A. Penfold, Jan Jakub Żylicz, John C. Marioni, Jamie A. Hackett, M. Azim Surani · 2017 · eLife
9. Single-Cell Transcriptional Analysis
   Angela Ruohao Wu, Jianbin Wang, Aaron Streets, Yanyi Huang · 2017 · Annual Review of Analytical Chemistry
10. The Arabidopsis SMALL AUXIN UP RNA32 Protein Regulates ABA-Mediated Responses to Drought Stress
    Yanjun He, Yue Liu, Mengzhuo Li, Anthony Tumbeh Lamin‐Samu, Dandan Yang, Xiaolin Yu, Izhar Muhammad, Ibadullah Jan, Muhammad Ali, Gang Lu · 2021 · Frontiers in Plant Science
11. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
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12. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
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13. Patch-seq: Past, Present, and Future
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14. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
    Tarik A. Khan, Simon Friedensohn, Arthur R. Gorter de Vries, Jakub Straszewski, Hans‐Joachim Ruscheweyh, Sai T. Reddy · 2016 · Science Advances
15. Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow
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16. qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide
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17. Studying hematopoiesis using single-cell technologies
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18. Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
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19. RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase
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20. Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel
    Sanushka Naidoo, Erik Andrei Visser, Lizahn Zwart, Yves du Toit, Vijai Bhadauria, Louise Simone Shuey · 2017 · Current Issues in Molecular Biology
21. Food allergen detection by mass spectrometry: the role of systems biology
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22. Beyond comparisons of means: understanding changes in gene expression at the single-cell level
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23. Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
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24. Mediation of Drosophilaautosomal dosage effects and compensation by network interactions
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25. The quest for absolute abundance: The use of internal standards for DNA‐based community ecology
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26. Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR
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27. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data
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28. RNA sequencing validation of the Complexity INdex in SARComas prognostic signature
    Tom Lesluyes, Gaëlle Pérot, Marine Roxane. Largeau, Céline Brulard, Pauline Lagarde, Valérie Dapremont, Carlo Lucchesi, Agnès Neuville, Philippe Terrier, Dominique Ranchère‐Vince et al. · 2016 · European Journal of Cancer
29. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes
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30. Ribosome profiling: a Hi‐Def monitor for protein synthesis at the genome‐wide scale
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31. Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
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32. Limitations of alignment-free tools in total RNA-seq quantification
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33. RNA-Seq Analysis of Transcriptome and Glucosinolate Metabolism in Seeds and Sprouts of Broccoli (Brassica oleracea var. italic)
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34. Determining the Contribution of Micro/Nanoplastics to Antimicrobial Resistance: Challenges and Perspectives
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35. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
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36. Bacteria differently regulate mRNA abundance to specifically respond to various stresses
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37. Differential contribution of p300 and CBP to regulatory element acetylation in mESCs
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38. Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses
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39. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research
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40. De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties
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41. Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors
    Julie W. Reeser, Dorrelyn Patacsil, Jharna Miya, Esko Antero Kautto, Ezra Lyon, Eliot Y. Zhu, Michele R. Wing, Amy M. Smith, Matthew Reeder, Eric Samorodnitsky et al. · 2017 · Journal of Molecular Diagnostics
42. Transcriptome Remodeling of Differentiated Cells during Chronological Ageing of Yeast Colonies: New Insights into Metabolic Differentiation
    Derek Wilkinson, Jana Maršíková, Otakar Hlaváček, Gregor D. Gilfillan, Eva Jezkova, Ragnhild Aaløkken, Libuše Váchová, Zdena Palková · 2018 · Oxidative Medicine and Cellular Longevity
43. A statistical simulator scDesign for rational scRNA-seq experimental design
    Wei Vivian Li, Jingyi Jessica Li · 2019 · Bioinformatics
44. Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing
    Farnoosh Abbas Aghababazadeh, Qian Li, Brooke L. Fridley · 2018 · PLoS ONE
45. ROTS: reproducible RNA-seq biomarker detector—prognostic markers for clear cell renal cell cancer
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46. Current, faltering, and future strategies for advancing microbiome-assisted sustainable agriculture and environmental resilience
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47. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction
    Zachary T. Herbert, Jamie P. Kershner, Vincent L. Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O. Alekseyev, Jun Fan, Jessica W. Podnar, Edward Wilcox, Jenny R. Gipson et al. · 2018 · BMC Genomics
48. Application of next generation qPCR and sequencing platforms to mRNA biomarker analysis
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49. Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process
    Dafu Ru, Yongshuai Sun, Donglei Wang, Yang Chen, Tianjing Wang, Quanjun Hu, Richard J. Abbott, Jianquan Liu · 2018 · Molecular Ecology
50. Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium
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51. Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome
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52. Single-Cell Genomics: Approaches and Utility in Immunology
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53. Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases
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54. Single‐cell RNA‐sequencing of the brain
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55. scRMD: imputation for single cell RNA-seq data via robust matrix decomposition
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56. Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells
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57. An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period
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58. Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data
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59. Quantitative single-cell transcriptomics
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60. spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
    Joachim De Jonghe, Tomasz S. Kamiński, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte E. Handford, Gregory M. Findlay, Magdalena Zernicka‐Goetz et al. · 2023 · Nature Communications
61. Transcriptomic comparison between developing seeds of yellow- and black-seeded Brassica napus reveals that genes influence seed quality
    Jinjin Jiang, Shuang Zhu, Yi Yuan, Yue Wang, Lei Zeng, Jacqueline Batley, You-Ping Wang · 2019 · BMC Plant Biology
62. Breast cancer biomarker measurements and standards
    Kenneth D. Cole, Hua‐Jun He, Lili Wang · 2012 · PROTEOMICS - CLINICAL APPLICATIONS
63. Data Analysis in Single-Cell Transcriptome Sequencing
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64. Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing
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65. ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms
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66. Robust detection of alternative splicing in a population of single cells
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67. Single-cell transcriptional profiling: a window into embryonic cell-type specification
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68. Transcriptional-translational conflict is a barrier to cellular transformation and cancer progression
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69. A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells
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70. Reducing bias in RNA sequencing data: a novel approach to compute counts
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71. Metagenomic Quantification of Genes with Internal Standards
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72. Comparative analysis of de novo transcriptome assembly
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73. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments
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74. Widespread hypertranscription in aggressive human cancers
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75. Systems vaccinology
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76. A brief review of single-cell transcriptomic technologies
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77. Re-annotation of eightDrosophilagenomes
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78. Goals and approaches for each processing step for single-cell RNA sequencing data
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79. Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing
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80. Identification of cardiac long non-coding RNA profile in human dilated cardiomyopathy
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81. NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data
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82. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation
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83. Canalized gene expression during development mediates caste differentiation in ants
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84. Conserved expression of natural antisense transcripts in mammals
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85. Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology
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86. DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data
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87. Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design
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88. S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data
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89. Aberrantly Expressed RECQL4 Helicase Supports Proliferation and Drug Resistance of Human Glioma Cells and Glioma Stem Cells
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90. Representing genetic variation with synthetic DNA standards
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91. The Histone Demethylase LSD1 Regulates B Cell Proliferation and Plasmablast Differentiation
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92. Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq
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93. Transcriptomic analysis of degraded forensic body fluids
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94. Normalization of RNA-Sequencing Data from Samples with Varying mRNA Levels
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95. Shedding light: The importance of reverse transcription efficiency standards in data interpretation
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96. Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
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97. TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling
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98. SIRVs: Spike-In RNA Variants as External Isoform Controls in RNA-Sequencing
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99. Molecular spikes: a gold standard for single-cell RNA counting
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100. Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming
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